Working with prealigned sequences

This page demonstrates a posibble workflow when dealing with prealigned sequences that we do not wish to realign, possibly because the method by which they were aligned is not availbale in ReproPhylo. In this case we wil analyse a SILVA alignment, which takes the secondary structure of the aligned sequences into consideration.

In [1]:
from reprophylo import *

The alignment consists of 18S rRNA sequences. We will start a project and define the the locus we are analysing:

In [2]:
pj = Project([Locus('dna','rRNA','18s',['18s'])])
In [3]:
print pj.loci[0]
Locus(char_type=dna, feature_type=rRNA, name=18s, aliases=18s)

In order to read an alignment and place it as such in the Project, we can use the Project method read_alignment.
Note: If we wanted to realign the sequences, we would then have read the same file with the read_denovo method, which would have reset the gaps and would place the data as sequence records instead of as a sequence alignment.

In [4]:
# Raising an error because of a mistake in the locus name
pj.read_alignment('data/arb-silva.de_2014-11-17_id215613_gapcompressedvertical.fasta','dna','rRNA','missing_locus')
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-4-906a5bba52cf> in <module>()
----> 1 pj.read_alignment('data/arb-silva.de_2014-11-17_id215613_gapcompressedvertical.fasta','dna','rRNA','missing_locus')

/home/amir/Dropbox/ReproPhylo/reprophylo.py in read_alignment(self, filename, char_type, feature_type, locus_name, format, aln_method_name, exclude)
    989 
    990         if not any([locus.name == locus_name for locus in self.loci]):
--> 991             raise RuntimeError("Locus %s does not exist"%locus_name)
    992         elif not [locus for locus in self.loci if locus.name == locus_name][0].char_type == char_type:
    993             raise RuntimeError("%s is not a %s locus"%(locus_name, char_type))

RuntimeError: Locus missing_locus does not exist
reprophylo.py:988: UserWarning: Version control off
  warnings.warn('Version control off')

In [5]:
# Raising an error because of an error in the feature type
pj.read_alignment('data/arb-silva.de_2014-11-17_id215613_gapcompressedvertical.fasta','dna','wrong_feature','18s')
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-5-99e3d0ea4cf1> in <module>()
----> 1 pj.read_alignment('data/arb-silva.de_2014-11-17_id215613_gapcompressedvertical.fasta','dna','wrong_feature','18s')

/home/amir/Dropbox/ReproPhylo/reprophylo.py in read_alignment(self, filename, char_type, feature_type, locus_name, format, aln_method_name, exclude)
    993             raise RuntimeError("%s is not a %s locus"%(locus_name, char_type))
    994         elif not [locus for locus in self.loci if locus.name == locus_name][0].feature_type == feature_type:
--> 995             raise RuntimeError("The feature_type %s is not %s"%(locus_name, feature_type))
    996 
    997         count = 0

RuntimeError: The feature_type 18s is not wrong_feature
In [6]:
# Raising an error because of an error in the character type
pj.read_alignment('data/arb-silva.de_2014-11-17_id215613_gapcompressedvertical.fasta','prot','rRNA','18s')
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-6-4d3cd65cc4a0> in <module>()
----> 1 pj.read_alignment('data/arb-silva.de_2014-11-17_id215613_gapcompressedvertical.fasta','prot','rRNA','18s')

/home/amir/Dropbox/ReproPhylo/reprophylo.py in read_alignment(self, filename, char_type, feature_type, locus_name, format, aln_method_name, exclude)
    991             raise RuntimeError("Locus %s does not exist"%locus_name)
    992         elif not [locus for locus in self.loci if locus.name == locus_name][0].char_type == char_type:
--> 993             raise RuntimeError("%s is not a %s locus"%(locus_name, char_type))
    994         elif not [locus for locus in self.loci if locus.name == locus_name][0].feature_type == feature_type:
    995             raise RuntimeError("The feature_type %s is not %s"%(locus_name, feature_type))

RuntimeError: 18s is not a prot locus
In [7]:
# Finaly getting it right
pj.read_alignment('data/arb-silva.de_2014-11-17_id215613_gapcompressedvertical.fasta','dna','rRNA','18s')
reprophylo.py:1044: UserWarning: To get translations, aff a feature manually
  warnings.warn("To get translations, aff a feature manually")

The read alignment places the data in several places. It will place degapped sequences as records in pj.records:

In [8]:
pj.records[:10]
Out[8]:
[SeqRecord(seq=Seq('AACGGCUCAUUACAAUAGCCAUUAUUUACUUGAUCUUGAUCAAUCCUAAAUGGA...ACU', IUPACAmbiguousDNA()), id='denovo0', name='denovo0', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('AACGGCUCAUUACAAUGGCCAUGAUUUACUUGAUCUUGAUUAAUCCUAAAUGGA...AUU', IUPACAmbiguousDNA()), id='denovo1', name='denovo1', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('AACGGCUCAUUACAAUGGCCAUGAUUUACUUGAUCUUGAUUAAUCCUAAAUGGA...AUU', IUPACAmbiguousDNA()), id='denovo2', name='denovo2', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('GGCGAUCAGAUACCGCCCUAGUUCUGACCGUAAACGAUGCCAACUAGCGAUCCG...GUA', IUPACAmbiguousDNA()), id='denovo3', name='denovo3', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('GGCGAUCAGAUACCGCCCUAGUUCUGACCGUAAACGAUGCCAACUAGCGAUCCG...GUA', IUPACAmbiguousDNA()), id='denovo4', name='denovo4', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('AUGUACCAGUUUAAUCGAUUUAUCGAGAAACCGCGAACGGCUCAUUACAAUGGC...GGC', IUPACAmbiguousDNA()), id='denovo5', name='denovo5', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('AUGUACCAGUUUAAUCGAUUUAUCGAGAAACCGCGAACGGCUCAUUACAAUGGC...GGC', IUPACAmbiguousDNA()), id='denovo6', name='denovo6', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('AACACGGGGAAACUCACCCGGCCCGGACACUGUGAGGAUUGACAGAUUGAUAGC...GGC', IUPACAmbiguousDNA()), id='denovo7', name='denovo7', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('AUGUACCAGUUUAAUCGAUUUAUCGAGAAACCGCGAACGGCUCAUUACAAUGGC...GGC', IUPACAmbiguousDNA()), id='denovo8', name='denovo8', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('AUGUACCAGUUUAAUCGAUUUAUCGAGAAACCGCGAACGGCUCAUUACAAUGGC...GGC', IUPACAmbiguousDNA()), id='denovo9', name='denovo9', description='<unknown description>', dbxrefs=[])]

The records will have a new source feature, as is the case when we read denovo data with read_denovo. However, unlike read_denovo, read_alignment will also add a normal sequence feature, with all the qualifiers usually add by ReproPhylo, such as feature_id and GC_content. The gene specified as an argument of read_alignment will be added to the gene qualifier of this new feature:

In [9]:
pj.write('starting_with_aln.gb')
In [10]:
genbank_file = !cat starting_with_aln.gb
for line in genbank_file[:100]:
    print line
LOCUS       denovo0                 1582 bp    DNA              UNK 01-JAN-1980
DEFINITION  .
ACCESSION   denovo0
VERSION     denovo0
KEYWORDS    .
SOURCE      .
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     source          1..1582
                     /feature_id="denovo0_source"
                     /original_id="AF442191.1.1582"
                     /original_desc="Eukaryota;Opisthokonta;Holozoa;Metazoa;Anim
                     alia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne
                     ichinohei"
     rRNA            1..1582
                     /feature_id="denovo0_f0"
                     /GC_content="48.6093552465"
                     /gene="18s"
                     /nuc_degen_prop="0.0"
ORIGIN
        1 aacggcucau uacaauagcc auuauuuacu ugaucuugau caauccuaaa uggauaacug
       61 uggaaaagcu agagcuaaua caugcacaaa agcuccgacc ccucggggga gagcguauuu
      121 auuggaacaa aaccaagcag cuucggcugu ucauuguuga cucagaauaa cucaacugac
      181 cgcacggccc cgagccggcg gcgugucauu caagugucua cuuuaucaua cuugauguua
      241 guaucagugg cuaacauggu ggugacggau aacggaggau caggguucga cuccggagaa
      301 ggggccugag aaauggccac uacgucuaag gauggcagca ggcgcgcaaa uuacccacuc
      361 ucggcaugag gagguaguga cgagaaauaa cgaggccguu cucuucugag gccggucauc
      421 ggaaugggaa aaauuuaaau ccuuuaucga guaucuacga gagggcaagu cuggugccag
      481 cagccgcggu aauuccagcu cucgaaguac cuaggaguau ugcugcgguu aaaaagcucg
      541 uaguuggacu uaaagucggu accguagucc cccuagggug cguacuacag uauugucuua
      601 cuguaauguu cugccuuggg ccuuuaacag ggaacucgcg cagucguuac aaguuuacuu
      661 ugaacaaauc agagugcuuc aaacaagcgg uucgcuugaa uguucgugca uggaauaaua
      721 gaagaggauu uugguucuau uuuauugguu uuauaggcug agauaauggu uaaaagagac
      781 aaacgggggu auucguaugg acacgugaga ggugaaauuc uuggaccgug gccagacgga
      841 cuacagcgaa agcauuugcc aagaaugucu ucauuaauca agaacgaaag ucagagguuc
      901 gaaggcgauc agauaccgcc cuaguucuga ccguaaacga ugccaacuag cgauccgccg
      961 auggaaauuu uugccuuggu ggggagcuuc ccggaaacga aagucuuccg guuccggggg
     1021 aaguaugguu gcaaagcuga aacuuaaagg aauugacgga agggcaccac caggagugga
     1081 gccugcggcu uaauuugacu caacacggga aaacucaccc ggcccggaca ccgucaggau
     1141 ugacagauug auagcuuuuu caugauucgg uggauggugg ugcauggccg uucuuaguuc
     1201 guggagugau uugucugguu uauuccgaua acgagcgaga cucucgccua cuaaauagcc
     1261 ggagcauugu uucugugcuu gcgacuucuu agagggauuu ucgguguuca gccgcaagaa
     1321 auugagcaau aacaggucug ugaugcccuu agauguccgg ggcugcacgc gcgcuacacu
     1381 ggcaaaauca gcgugcuugu ccuccuccga aaggaguugg uaaaccccug aaaauuugcc
     1441 gugauaggga ucggaaauug caauuauuuu ccgugaacga ggaauuccaa guaagugcga
     1501 gucaucagcu cgcguugauu acgucccugc ccuuuguaca caccgcccgu cgcugcccgg
     1561 gacugagcca uuucgagaaa cu
//
LOCUS       denovo1                 1578 bp    DNA              UNK 01-JAN-1980
DEFINITION  .
ACCESSION   denovo1
VERSION     denovo1
KEYWORDS    .
SOURCE      .
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     source          1..1578
                     /feature_id="denovo1_source"
                     /original_id="AF442195.1.1578"
                     /original_desc="Eukaryota;Opisthokonta;Holozoa;Metazoa;Anim
                     alia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne
                     chitwoodi"
     rRNA            1..1578
                     /feature_id="denovo1_f0"
                     /GC_content="47.0215462611"
                     /gene="18s"
                     /nuc_degen_prop="0.0"
ORIGIN
        1 aacggcucau uacaauggcc augauuuacu ugaucuugau uaauccuaaa uggauaacug
       61 uggaaaaucu agagcuaaua caugcacuaa agcuuugacc ucacggaaaa gcgcauuuau
      121 uagaacaaaa ccacgcggcu ucggcugcuc uuuguugacu cagaauaacu aagcugaccg
      181 cauggccuug ugccggcggc gugucuuuca agcguccacu uuaucaacuu gacgggagca
      241 uaaucgacuc ccgugguugu gacggauaac ggaggaucag gguucgacuc cggagaaggg
      301 gccugagaaa uggccacuac gucuaaggau ggcagcaggc gcgcaaauua cccacucucg
      361 gcucgaggag guagugacga gaaauaacga gaccguucuc auugaggccg gucaucggaa
      421 uggguacaau uuaaacccuu uaacgaguau caaggagagg gcaagucugg ugccagcagc
      481 cgcgguaauu ccagcuuucc uaaugcauag aauuauugcu gcgguuaaaa agcucguagu
      541 uggauucgua ucgauacucu ggaacccuuc ggguguuucu ggauguuauc gauuuaucgu
      601 aauguucagu uuugaguccu uaacaggauu cuuaacaggc auugcaaguu uacuuugaac
      661 aaaucagagu gcuucaaaca ggcguuucgc uugaaugauc gugcauggaa uaauagaaaa
      721 cgauuucggu ucaguuuuau ugguuuuacg gacugagaua augguuaaca gagacaaacg
      781 ggggcauuug uauggccccg ugagagguga aauucuugga ccguggccag acaaacuaca
      841 gcgaaagcau uugccaagaa ugucuucauu aaucaagaac gaaagucaga gguucgaagg
      901 cgaucagaua ccgcccuagu ucugaccgua aacgaugcca acuagcgauc cgccgaugga
      961 gauuauauug ccuugguggg gagcuucccg gaaacgaaag ucuuccgguu ccgggggaag
     1021 uaugguugca aagcugaaac uuaaaggaau ugacggaagg gcaccaccag gaguggagcc
     1081 ugcggcuuaa uuugacucaa cacgggaaaa cucacccggc ccggacacug ugaggauuga
     1141 cagauugaua gcuuuuucau gauucagugg augguggugc auggccguuc uuaguucgug
     1201 gagugauuug ucugguuuau uccgauaacg agcgagacuc uaaccuacua aauaguugau
     1261 auuuuuuuuu gaauauacaa cuucuuagag ggauuugcgg uguuuagccg aaagaaauug
     1321 agcaauaaca ggucugugau gcccuuagau guccggggcu gcacgcgcgc uacacuggca
     1381 aaaucaacgu gcuuguccuu ccccgaaagg ggcggguaaa ccauugaaaa uuugccguga
     1441 uugggaucgg aaauugcaau uauuuuccgu gaacgaggaa uuccaaguaa gugcgaguca
     1501 ucagcucgcg uugauuacgu cccugcccuu uguacacacc gcccgucgcu gcccgggacu
     1561 gagccauuuc gagaaauu
//
LOCUS       denovo2                 1581 bp    DNA              UNK 01-JAN-1980
DEFINITION  .

and as expected, the alignment object will be added to pj.alignments:

In [11]:
print pj.alignments['18s@ReadDirectly']
IUPACAmbiguousDNA() alignment with 291 rows and 2426 columns
--------------------------------------------...--- denovo0_f0
--------------------------------------------...--- denovo1_f0
--------------------------------------------...--- denovo2_f0
--------------------------------------------...--- denovo3_f0
--------------------------------------------...--- denovo4_f0
--------------------------------------------...--- denovo5_f0
--------------------------------------------...--- denovo6_f0
--------------------------------------------...--- denovo7_f0
--------------------------------------------...--- denovo8_f0
--------------------------------------------...--- denovo9_f0
--------------------------------------------...--- denovo10_f0
---UCUGGUUGAUCCUGCCUGAACUGAUGUGUUCAUUUCAAAG-...--- denovo11_f0
--------------------------------------------...--- denovo12_f0
--------------------------------------------...--- denovo13_f0
--------------------------------------------...--- denovo14_f0
---CCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAA-AG...--- denovo15_f0
---UCUGGUUGAUCCUGCCUGAACUGAUGUGUUCAUUUCAAAG-...--- denovo16_f0
--------------------------------------------...--- denovo17_f0
...
--------------------------------------------...--- denovo290_f0

Using the show_aln method, we can now view the sequence alignment graphically. To make it informative we'll use the original description as labels. A small slice of the screen is pesented below.

In [12]:
pj.show_aln('18s@ReadDirectly', id=['source_original_desc'])
In [37]:
from IPython.display import Image
Image('Selection_011.png', width='700')
Out[37]:

Well, the original description is not very convinient as it is too long. We have to edit the metadata a bit, either by printing a metadata CSV file, editing it and reading it back (see Tetillidae tutorial) or using Project method. We will copy the original description from the source features to the sequence features:

In [18]:
pj.add_qualifier_from_source('original_desc')

Let's see if it worked:

In [14]:
pj.write('starting_with_aln.gb')
In [15]:
genbank_file = !cat starting_with_aln.gb
for line in genbank_file[:100]:
    print line
LOCUS       denovo0                 1582 bp    DNA              UNK 01-JAN-1980
DEFINITION  .
ACCESSION   denovo0
VERSION     denovo0
KEYWORDS    .
SOURCE      .
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     source          1..1582
                     /feature_id="denovo0_source"
                     /original_id="AF442191.1.1582"
                     /original_desc="Eukaryota;Opisthokonta;Holozoa;Metazoa;Anim
                     alia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne
                     ichinohei"
     rRNA            1..1582
                     /feature_id="denovo0_f0"
                     /GC_content="48.6093552465"
                     /gene="18s"
                     /nuc_degen_prop="0.0"
                     /original_desc="Eukaryota;Opisthokonta;Holozoa;Metazoa;Anim
                     alia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne
                     ichinohei"
ORIGIN
        1 aacggcucau uacaauagcc auuauuuacu ugaucuugau caauccuaaa uggauaacug
       61 uggaaaagcu agagcuaaua caugcacaaa agcuccgacc ccucggggga gagcguauuu
      121 auuggaacaa aaccaagcag cuucggcugu ucauuguuga cucagaauaa cucaacugac
      181 cgcacggccc cgagccggcg gcgugucauu caagugucua cuuuaucaua cuugauguua
      241 guaucagugg cuaacauggu ggugacggau aacggaggau caggguucga cuccggagaa
      301 ggggccugag aaauggccac uacgucuaag gauggcagca ggcgcgcaaa uuacccacuc
      361 ucggcaugag gagguaguga cgagaaauaa cgaggccguu cucuucugag gccggucauc
      421 ggaaugggaa aaauuuaaau ccuuuaucga guaucuacga gagggcaagu cuggugccag
      481 cagccgcggu aauuccagcu cucgaaguac cuaggaguau ugcugcgguu aaaaagcucg
      541 uaguuggacu uaaagucggu accguagucc cccuagggug cguacuacag uauugucuua
      601 cuguaauguu cugccuuggg ccuuuaacag ggaacucgcg cagucguuac aaguuuacuu
      661 ugaacaaauc agagugcuuc aaacaagcgg uucgcuugaa uguucgugca uggaauaaua
      721 gaagaggauu uugguucuau uuuauugguu uuauaggcug agauaauggu uaaaagagac
      781 aaacgggggu auucguaugg acacgugaga ggugaaauuc uuggaccgug gccagacgga
      841 cuacagcgaa agcauuugcc aagaaugucu ucauuaauca agaacgaaag ucagagguuc
      901 gaaggcgauc agauaccgcc cuaguucuga ccguaaacga ugccaacuag cgauccgccg
      961 auggaaauuu uugccuuggu ggggagcuuc ccggaaacga aagucuuccg guuccggggg
     1021 aaguaugguu gcaaagcuga aacuuaaagg aauugacgga agggcaccac caggagugga
     1081 gccugcggcu uaauuugacu caacacggga aaacucaccc ggcccggaca ccgucaggau
     1141 ugacagauug auagcuuuuu caugauucgg uggauggugg ugcauggccg uucuuaguuc
     1201 guggagugau uugucugguu uauuccgaua acgagcgaga cucucgccua cuaaauagcc
     1261 ggagcauugu uucugugcuu gcgacuucuu agagggauuu ucgguguuca gccgcaagaa
     1321 auugagcaau aacaggucug ugaugcccuu agauguccgg ggcugcacgc gcgcuacacu
     1381 ggcaaaauca gcgugcuugu ccuccuccga aaggaguugg uaaaccccug aaaauuugcc
     1441 gugauaggga ucggaaauug caauuauuuu ccgugaacga ggaauuccaa guaagugcga
     1501 gucaucagcu cgcguugauu acgucccugc ccuuuguaca caccgcccgu cgcugcccgg
     1561 gacugagcca uuucgagaaa cu
//
LOCUS       denovo1                 1578 bp    DNA              UNK 01-JAN-1980
DEFINITION  .
ACCESSION   denovo1
VERSION     denovo1
KEYWORDS    .
SOURCE      .
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     source          1..1578
                     /feature_id="denovo1_source"
                     /original_id="AF442195.1.1578"
                     /original_desc="Eukaryota;Opisthokonta;Holozoa;Metazoa;Anim
                     alia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne
                     chitwoodi"
     rRNA            1..1578
                     /feature_id="denovo1_f0"
                     /GC_content="47.0215462611"
                     /gene="18s"
                     /nuc_degen_prop="0.0"
                     /original_desc="Eukaryota;Opisthokonta;Holozoa;Metazoa;Anim
                     alia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne
                     chitwoodi"
ORIGIN
        1 aacggcucau uacaauggcc augauuuacu ugaucuugau uaauccuaaa uggauaacug
       61 uggaaaaucu agagcuaaua caugcacuaa agcuuugacc ucacggaaaa gcgcauuuau
      121 uagaacaaaa ccacgcggcu ucggcugcuc uuuguugacu cagaauaacu aagcugaccg
      181 cauggccuug ugccggcggc gugucuuuca agcguccacu uuaucaacuu gacgggagca
      241 uaaucgacuc ccgugguugu gacggauaac ggaggaucag gguucgacuc cggagaaggg
      301 gccugagaaa uggccacuac gucuaaggau ggcagcaggc gcgcaaauua cccacucucg
      361 gcucgaggag guagugacga gaaauaacga gaccguucuc auugaggccg gucaucggaa
      421 uggguacaau uuaaacccuu uaacgaguau caaggagagg gcaagucugg ugccagcagc
      481 cgcgguaauu ccagcuuucc uaaugcauag aauuauugcu gcgguuaaaa agcucguagu
      541 uggauucgua ucgauacucu ggaacccuuc ggguguuucu ggauguuauc gauuuaucgu
      601 aauguucagu uuugaguccu uaacaggauu cuuaacaggc auugcaaguu uacuuugaac
      661 aaaucagagu gcuucaaaca ggcguuucgc uugaaugauc gugcauggaa uaauagaaaa
      721 cgauuucggu ucaguuuuau ugguuuuacg gacugagaua augguuaaca gagacaaacg
      781 ggggcauuug uauggccccg ugagagguga aauucuugga ccguggccag acaaacuaca
      841 gcgaaagcau uugccaagaa ugucuucauu aaucaagaac gaaagucaga gguucgaagg
      901 cgaucagaua ccgcccuagu ucugaccgua aacgaugcca acuagcgauc cgccgaugga
      961 gauuauauug ccuugguggg gagcuucccg gaaacgaaag ucuuccgguu ccgggggaag
     1021 uaugguugca aagcugaaac uuaaaggaau ugacggaagg gcaccaccag gaguggagcc
     1081 ugcggcuuaa uuugacucaa cacgggaaaa cucacccggc ccggacacug ugaggauuga
     1141 cagauugaua gcuuuuucau gauucagugg augguggugc auggccguuc uuaguucgug
     1201 gagugauuug ucugguuuau uccgauaacg agcgagacuc uaaccuacua aauaguugau
     1261 auuuuuuuuu gaauauacaa cuucuuagag ggauuugcgg uguuuagccg aaagaaauug
     1321 agcaauaaca ggucugugau gcccuuagau guccggggcu gcacgcgcgc uacacuggca
     1381 aaaucaacgu gcuuguccuu ccccgaaagg ggcggguaaa ccauugaaaa uuugccguga

Now we have the descriptions in the feature's qualifiers. Let's use actual Biopython to turn them to concise 'organism' qualifiers:

In [19]:
for record in pj.records:
    for feature in record.features:
        feature.qualifiers['organism'] = [feature.qualifiers['original_desc'][0].split(';')[-1]]

Now we'll check again if our new qualifier was added to the features:

In [17]:
pj.write('starting_with_aln.gb')
In [18]:
genbank_file = !cat starting_with_aln.gb
for line in genbank_file[:100]:
    print line
LOCUS       denovo0                 1582 bp    DNA              UNK 01-JAN-1980
DEFINITION  .
ACCESSION   denovo0
VERSION     denovo0
KEYWORDS    .
SOURCE      .
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     source          1..1582
                     /feature_id="denovo0_source"
                     /organism="Meloidogyne ichinohei"
                     /original_id="AF442191.1.1582"
                     /original_desc="Eukaryota;Opisthokonta;Holozoa;Metazoa;Anim
                     alia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne
                     ichinohei"
     rRNA            1..1582
                     /nuc_degen_prop="0.0"
                     /feature_id="denovo0_f0"
                     /original_desc="Eukaryota;Opisthokonta;Holozoa;Metazoa;Anim
                     alia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne
                     ichinohei"
                     /GC_content="48.6093552465"
                     /gene="18s"
                     /organism="Meloidogyne ichinohei"
ORIGIN
        1 aacggcucau uacaauagcc auuauuuacu ugaucuugau caauccuaaa uggauaacug
       61 uggaaaagcu agagcuaaua caugcacaaa agcuccgacc ccucggggga gagcguauuu
      121 auuggaacaa aaccaagcag cuucggcugu ucauuguuga cucagaauaa cucaacugac
      181 cgcacggccc cgagccggcg gcgugucauu caagugucua cuuuaucaua cuugauguua
      241 guaucagugg cuaacauggu ggugacggau aacggaggau caggguucga cuccggagaa
      301 ggggccugag aaauggccac uacgucuaag gauggcagca ggcgcgcaaa uuacccacuc
      361 ucggcaugag gagguaguga cgagaaauaa cgaggccguu cucuucugag gccggucauc
      421 ggaaugggaa aaauuuaaau ccuuuaucga guaucuacga gagggcaagu cuggugccag
      481 cagccgcggu aauuccagcu cucgaaguac cuaggaguau ugcugcgguu aaaaagcucg
      541 uaguuggacu uaaagucggu accguagucc cccuagggug cguacuacag uauugucuua
      601 cuguaauguu cugccuuggg ccuuuaacag ggaacucgcg cagucguuac aaguuuacuu
      661 ugaacaaauc agagugcuuc aaacaagcgg uucgcuugaa uguucgugca uggaauaaua
      721 gaagaggauu uugguucuau uuuauugguu uuauaggcug agauaauggu uaaaagagac
      781 aaacgggggu auucguaugg acacgugaga ggugaaauuc uuggaccgug gccagacgga
      841 cuacagcgaa agcauuugcc aagaaugucu ucauuaauca agaacgaaag ucagagguuc
      901 gaaggcgauc agauaccgcc cuaguucuga ccguaaacga ugccaacuag cgauccgccg
      961 auggaaauuu uugccuuggu ggggagcuuc ccggaaacga aagucuuccg guuccggggg
     1021 aaguaugguu gcaaagcuga aacuuaaagg aauugacgga agggcaccac caggagugga
     1081 gccugcggcu uaauuugacu caacacggga aaacucaccc ggcccggaca ccgucaggau
     1141 ugacagauug auagcuuuuu caugauucgg uggauggugg ugcauggccg uucuuaguuc
     1201 guggagugau uugucugguu uauuccgaua acgagcgaga cucucgccua cuaaauagcc
     1261 ggagcauugu uucugugcuu gcgacuucuu agagggauuu ucgguguuca gccgcaagaa
     1321 auugagcaau aacaggucug ugaugcccuu agauguccgg ggcugcacgc gcgcuacacu
     1381 ggcaaaauca gcgugcuugu ccuccuccga aaggaguugg uaaaccccug aaaauuugcc
     1441 gugauaggga ucggaaauug caauuauuuu ccgugaacga ggaauuccaa guaagugcga
     1501 gucaucagcu cgcguugauu acgucccugc ccuuuguaca caccgcccgu cgcugcccgg
     1561 gacugagcca uuucgagaaa cu
//
LOCUS       denovo1                 1578 bp    DNA              UNK 01-JAN-1980
DEFINITION  .
ACCESSION   denovo1
VERSION     denovo1
KEYWORDS    .
SOURCE      .
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     source          1..1578
                     /feature_id="denovo1_source"
                     /organism="Meloidogyne chitwoodi"
                     /original_id="AF442195.1.1578"
                     /original_desc="Eukaryota;Opisthokonta;Holozoa;Metazoa;Anim
                     alia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne
                     chitwoodi"
     rRNA            1..1578
                     /nuc_degen_prop="0.0"
                     /feature_id="denovo1_f0"
                     /original_desc="Eukaryota;Opisthokonta;Holozoa;Metazoa;Anim
                     alia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne
                     chitwoodi"
                     /GC_content="47.0215462611"
                     /gene="18s"
                     /organism="Meloidogyne chitwoodi"
ORIGIN
        1 aacggcucau uacaauggcc augauuuacu ugaucuugau uaauccuaaa uggauaacug
       61 uggaaaaucu agagcuaaua caugcacuaa agcuuugacc ucacggaaaa gcgcauuuau
      121 uagaacaaaa ccacgcggcu ucggcugcuc uuuguugacu cagaauaacu aagcugaccg
      181 cauggccuug ugccggcggc gugucuuuca agcguccacu uuaucaacuu gacgggagca
      241 uaaucgacuc ccgugguugu gacggauaac ggaggaucag gguucgacuc cggagaaggg
      301 gccugagaaa uggccacuac gucuaaggau ggcagcaggc gcgcaaauua cccacucucg
      361 gcucgaggag guagugacga gaaauaacga gaccguucuc auugaggccg gucaucggaa
      421 uggguacaau uuaaacccuu uaacgaguau caaggagagg gcaagucugg ugccagcagc
      481 cgcgguaauu ccagcuuucc uaaugcauag aauuauugcu gcgguuaaaa agcucguagu
      541 uggauucgua ucgauacucu ggaacccuuc ggguguuucu ggauguuauc gauuuaucgu
      601 aauguucagu uuugaguccu uaacaggauu cuuaacaggc auugcaaguu uacuuugaac
      661 aaaucagagu gcuucaaaca ggcguuucgc uugaaugauc gugcauggaa uaauagaaaa
      721 cgauuucggu ucaguuuuau ugguuuuacg gacugagaua augguuaaca gagacaaacg
      781 ggggcauuug uauggccccg ugagagguga aauucuugga ccguggccag acaaacuaca
      841 gcgaaagcau uugccaagaa ugucuucauu aaucaagaac gaaagucaga gguucgaagg
      901 cgaucagaua ccgcccuagu ucugaccgua aacgaugcca acuagcgauc cgccgaugga
      961 gauuauauug ccuugguggg gagcuucccg gaaacgaaag ucuuccgguu ccgggggaag
     1021 uaugguugca aagcugaaac uuaaaggaau ugacggaagg gcaccaccag gaguggagcc
     1081 ugcggcuuaa uuugacucaa cacgggaaaa cucacccggc ccggacacug ugaggauuga
     1141 cagauugaua gcuuuuucau gauucagugg augguggugc auggccguuc uuaguucgug

OK, we can now use the 'organism' qualifiers as labels to make a reasonablly looking sequence alignment:

In [19]:
pj.show_aln('18s@ReadDirectly', id=['organism'])
In [35]:
from IPython.display import Image
Image('Selection_009.png', width='700')
Out[35]:

Next step, alignemnt trimming (see Tetillidae tutorial):

In [13]:
manual = TrimalConf(pj, method_name='manual' ,trimal_commands={'gapthreshold': '0.5'})
trimal -in 318891416255164.58_18s@ReadDirectly.fasta -gapthreshold 0.5

In [14]:
pj.trim([manual])

Checking out the alignment will confirm the trimming took place:

In [29]:
pj.show_aln('18s@ReadDirectly@manual', id=['organism'])
In [39]:
from IPython.display import Image
Image('Selection_010.png', width='700')
Out[39]:

And tree reconstruction (again, see more details in the Tetillidae tutorial):

In [15]:
raxml = RaxmlConf(pj, method_name='fD_fb', preset='fD_fb', threads=6)
raxmlHPC-PTHREADS-SSE3 -f D -m GTRGAMMA -n 815311416255180.78_18s@ReadDirectly@manual0 -p 222 -s 815311416255180.78_18s@ReadDirectly@manual.fasta -T 6 -N 1
raxmlHPC-PTHREADS-SSE3 -f b -m GTRGAMMA -n 815311416255180.78_18s@ReadDirectly@manual1 -p 395 -s 815311416255180.78_18s@ReadDirectly@manual.fasta -t RAxML_bestTree.815311416255180.78_18s@ReadDirectly@manual0 -T 6 -z RAxML_rellBootstrap.815311416255180.78_18s@ReadDirectly@manual0

In [16]:
pj.tree([raxml])

The resulting tree will be rooted at midpoint and annotated with node supports:

In [20]:
supports = {'black':[100,99],
            'dimgray':[99,75],
            'silver':[75,50]}
pj.annotate('.', 'mid', 'mid', ['organism'], node_support_dict=supports, scale=2000)
<html>
rooting tree 18s@ReadDirectly@manual@fD_fb at midpoint
<A href=./815311416255180.78_18s@ReadDirectly@manual.png>815311416255180.78_18s@ReadDirectly@manual</A><BR>
</html>
.

Rather than viewing the png file, we can show the figure inline by fetching the tree object with the Project ft method and then render it with ETE's render method:

In [21]:
# The tree object retains the faces but not the tree style
# We need to exclude leaf names, but not the text faces or
# the brach support faces.
# We also do not get the supports legend
tstyle = TreeStyle()
tstyle.show_leaf_name = False

pj.ft('18s').render('%%inline', w=400, tree_style=tstyle)
returning tree object 18s@ReadDirectly@manual@fD_fb

Out[21]:
Generated with ETE http://ete.cgenomics.org Generated with ETE http://ete.cgenomics.org Meloidogyne hapla Meloidogyne hapla Meloidogyne sp. DLL-2013a Meloidogyne hapla Meloidogyne sp. DLL-2013c Meloidogyne hapla Meloidogyne hapla Meloidogyne sp. DLL-2013b Meloidogyne sp. DLL-2013d Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne hapla Meloidogyne partityla Meloidogyne partityla Meloidogyne dunensis Meloidogyne spartinae Meloidogyne cf. graminis TSH-2004 Meloidogyne marylandi Meloidogyne marylandi Meloidogyne marylandi Meloidogyne marylandi Meloidogyne marylandi Meloidogyne marylandi Meloidogyne cf. graminis TSH-2005 Meloidogyne cf. graminis TSH-2005 Meloidogyne cf. graminis TSH-2004 Meloidogyne graminis Meloidogyne graminis Meloidogyne graminis Meloidogyne graminis Meloidogyne graminis Meloidogyne graminis Meloidogyne graminis Meloidogyne graminis Meloidogyne graminis Meloidogyne graminis Meloidogyne graminis Meloidogyne graminis Meloidogyne maritima Meloidogyne maritima Meloidogyne maritima Meloidogyne microtyla Meloidogyne ardenensis Meloidogyne ardenensis Meloidogyne silvestris Meloidogyne hapla Meloidogyne duytsi Meloidogyne hapla Meloidogyne hapla Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne sp. Pak.P.R.37 Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne mayaguensis Meloidogyne mayaguensis Meloidogyne mayaguensis Meloidogyne mayaguensis Meloidogyne mayaguensis Meloidogyne mayaguensis Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne artiellia Meloidogyne artiellia Meloidogyne artiellia Meloidogyne artiellia Meloidogyne mali Meloidogyne mali Meloidogyne mali Meloidogyne mali Meloidogyne mali Meloidogyne mali Meloidogyne mali Meloidogyne mali Meloidogyne mali Meloidogyne sp. MHMH-2008 Meloidogyne sp. MHMH-2008 Meloidogyne sp. MHMH-2008 Meloidogyne coffeicola Meloidogyne camelliae Meloidogyne ichinohei Meloidogyne ichinohei Meloidogyne ichinohei Meloidogyne ichinohei Meloidogyne ichinohei Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne ethiopica Meloidogyne haplanaria Meloidogyne haplanaria Meloidogyne ethiopica Meloidogyne ethiopica Meloidogyne ethiopica Meloidogyne ethiopica Meloidogyne hispanica Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne ethiopica Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne hispanica Meloidogyne hispanica Meloidogyne hispanica Meloidogyne incognita (southern root-knot nematode) Meloidogyne sp. 38 Meloidogyne ethiopica Meloidogyne javanica (root-knot nematode) Meloidogyne ethiopica Meloidogyne incognita (southern root-knot nematode) Meloidogyne arabicida Meloidogyne arabicida Meloidogyne konaensis Meloidogyne paranaensis Meloidogyne izalcoensis Meloidogyne sp. MS3 Meloidogyne javanica (root-knot nematode) Meloidogyne sp. AC-2011 Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne sp. AC-2011 Meloidogyne incognita (southern root-knot nematode) Meloidogyne arenaria Meloidogyne javanica (root-knot nematode) Meloidogyne cf. arenaria TSH-2004 Meloidogyne cf. incognita TSH-2004 Meloidogyne cf. arenaria TSH-2004 Meloidogyne incognita (southern root-knot nematode) Meloidogyne hapla Meloidogyne javanica (root-knot nematode) Meloidogyne javanica (root-knot nematode) Meloidogyne cf. incognita TSH-2004 Meloidogyne cf. arenaria TSH-2004 Meloidogyne cf. incognita TSH-2005 Meloidogyne javanica (root-knot nematode) Meloidogyne javanica (root-knot nematode) Meloidogyne morocciensis Meloidogyne sp. Pak.P.R.m2 Meloidogyne sp. Pak.S.R.25 Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne javanica (root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne javanica (root-knot nematode) Meloidogyne sp. 50 Meloidogyne arenaria Meloidogyne incognita (southern root-knot nematode) Meloidogyne floridensis Meloidogyne arenaria Meloidogyne javanica (root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne sp. 40 Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne arenaria Meloidogyne javanica (root-knot nematode) Meloidogyne sp. AC-2011 Meloidogyne arenaria Meloidogyne arenaria Meloidogyne hapla Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne cf. incognita TSH-2004 Meloidogyne sp. AC-2011 Meloidogyne sp. AC-2011 Meloidogyne sp. AC-2011 Meloidogyne sp. AC-2011 Meloidogyne incognita (southern root-knot nematode) Meloidogyne javanica (root-knot nematode) Meloidogyne incognita (southern root-knot nematode) Meloidogyne sp. Brito DPI I Meloidogyne mayaguensis Meloidogyne exigua Meloidogyne exigua Meloidogyne exigua Meloidogyne oryzae Meloidogyne graminicola Meloidogyne cf. graminicola TSH-2005 Meloidogyne cf. graminicola TSH-2005 Meloidogyne cf. graminicola TSH-2005 Meloidogyne cf. graminicola TSH-2005 Meloidogyne cf. graminicola TSH-2005 Meloidogyne cf. graminicola TSH-2004 Meloidogyne graminicola Meloidogyne naasi Meloidogyne naasi Meloidogyne naasi Meloidogyne naasi Meloidogyne naasi Meloidogyne naasi Meloidogyne naasi Meloidogyne naasi Meloidogyne naasi Meloidogyne naasi Meloidogyne naasi Meloidogyne naasi Meloidogyne naasi Meloidogyne minor Meloidogyne minor Meloidogyne minor Meloidogyne minor Meloidogyne minor Meloidogyne minor Meloidogyne minor Meloidogyne minor Meloidogyne chitwoodi Meloidogyne fallax Meloidogyne fallax Meloidogyne fallax Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne fallax Meloidogyne fallax Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne fallax Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne cf. fallax TSH-2004 Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne cf. chitwoodi TSH-2004 Meloidogyne cf. chitwoodi TSH-2005 Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi Meloidogyne chitwoodi 0.11 0.11

Evaluate the analysis and repeat

It seems that we have some srange looking long branches in the tree. Lets use the full description as label to see the taxonomy of our OTUs and spot contaminations that were indicated in the SILVA description:

In [24]:
pj.clear_tree_annotations()
pj.annotate('.', 'mid', 'mid', ['source_original_desc'], node_support_dict=supports, scale=2000)
<html>
rooting tree 18s@ReadDirectly@manual@fD_fb at midpoint
<A href=./815311416255180.78_18s@ReadDirectly@manual.png>815311416255180.78_18s@ReadDirectly@manual</A><BR>
</html>
.

In [26]:
pj.ft('18s').render('%%inline', w=800, tree_style=tstyle)
returning tree object 18s@ReadDirectly@manual@fD_fb

Out[26]:
Generated with ETE http://ete.cgenomics.org Generated with ETE http://ete.cgenomics.org Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. DLL-2013a Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Brassicales;Arabidopsis;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. DLL-2013c Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. DLL-2013b Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. DLL-2013d Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne partityla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne partityla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne dunensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne spartinae Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. graminis TSH-2004 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne marylandi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne marylandi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne marylandi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne marylandi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne marylandi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne marylandi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. graminis TSH-2005 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. graminis TSH-2005 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. graminis TSH-2004 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne maritima Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne maritima Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne maritima Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne microtyla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ardenensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ardenensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne silvestris Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne duytsi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. Pak.P.R.37 Eukaryota;Opisthokonta;Nucletmycea;Fungi;Dikarya;Ascomycota;Pezizomycotina;Dothideomycetes;Capnodiales;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mayaguensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mayaguensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mayaguensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mayaguensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mayaguensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mayaguensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne artiellia Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne artiellia Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne artiellia Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne artiellia Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mali Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mali Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mali Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mali Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mali Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mali Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mali Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mali Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mali Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. MHMH-2008 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. MHMH-2008 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. MHMH-2008 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Meloidogyne coffeicola Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Meloidogyne camelliae Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ichinohei Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ichinohei Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ichinohei Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ichinohei Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ichinohei Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ethiopica Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne haplanaria Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne haplanaria Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ethiopica Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ethiopica Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ethiopica Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ethiopica Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hispanica Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ethiopica Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hispanica Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hispanica Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hispanica Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. 38 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ethiopica Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne javanica (root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne ethiopica Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne arabicida Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne arabicida Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne konaensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne paranaensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne izalcoensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. MS3 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne javanica (root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. AC-2011 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. AC-2011 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne arenaria Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne javanica (root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. arenaria TSH-2004 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. incognita TSH-2004 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. arenaria TSH-2004 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne javanica (root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne javanica (root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. incognita TSH-2004 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. arenaria TSH-2004 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. incognita TSH-2005 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne javanica (root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne javanica (root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne morocciensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. Pak.P.R.m2 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. Pak.S.R.25 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne javanica (root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne javanica (root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. 50 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne arenaria Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne floridensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne arenaria Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne javanica (root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. 40 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne arenaria Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne javanica (root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. AC-2011 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne arenaria Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne arenaria Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne hapla Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. incognita TSH-2004 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. AC-2011 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. AC-2011 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. AC-2011 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. AC-2011 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne javanica (root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne incognita (southern root-knot nematode) Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne sp. Brito DPI I Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne mayaguensis Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne exigua Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne exigua Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne exigua Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne oryzae Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminicola Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. graminicola TSH-2005 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. graminicola TSH-2005 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. graminicola TSH-2005 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. graminicola TSH-2005 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. graminicola TSH-2005 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. graminicola TSH-2004 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne graminicola Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne naasi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne naasi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne naasi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne naasi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne naasi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne naasi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne naasi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne naasi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne naasi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne naasi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne naasi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne naasi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne naasi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne minor Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne minor Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne minor Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne minor Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne minor Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne minor Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne minor Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne minor Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne fallax Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne fallax Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne fallax Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne fallax Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne fallax Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne fallax Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. fallax TSH-2004 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. chitwoodi TSH-2004 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne cf. chitwoodi TSH-2005 Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi Eukaryota;Opisthokonta;Holozoa;Metazoa;Animalia;Nematoda;Chromadorea;Heteroderidae;Meloidogyne chitwoodi 0.11 0.11

There are two branches indicated to be a contamination and another one where the branch is long and the species is not identified. We are going to print the tree again, using the organism and the original SILVA id to help us list the IDs of the sequence we want to exclude. We will be able to use this list in the read_alignment method to automatically exclude them without actually editing the input alignment file.

In [29]:
pj.clear_tree_annotations()
pj.annotate('.', 'mid', 'mid', ['organism','source_original_id'], node_support_dict=supports, scale=2000)
<html>
rooting tree 18s@ReadDirectly@manual@fD_fb at midpoint
<A href=./815311416255180.78_18s@ReadDirectly@manual.png>815311416255180.78_18s@ReadDirectly@manual</A><BR>
</html>
.

In [30]:
pj.ft('18s').render('%%inline', w=800, tree_style=tstyle)
returning tree object 18s@ReadDirectly@manual@fD_fb

Out[30]:
Generated with ETE http://ete.cgenomics.org Generated with ETE http://ete.cgenomics.org Meloidogyne hapla AY268119.1.1758 Meloidogyne hapla AY593892.1.1686 Meloidogyne sp. DLL-2013a KC545962.1.879 Meloidogyne hapla ABLG01003097.925.2722 Meloidogyne sp. DLL-2013c KC545964.1.878 Meloidogyne hapla AY942628.1.1660 Meloidogyne hapla EU669942.1.1685 Meloidogyne sp. DLL-2013b KC545963.1.880 Meloidogyne sp. DLL-2013d KC545965.1.884 Meloidogyne hapla KC545968.1.880 Meloidogyne hapla AY919174.1.636 Meloidogyne hapla AY919175.1.636 Meloidogyne hapla AY919176.1.636 Meloidogyne hapla AY757858.1.636 Meloidogyne hapla AY757863.1.636 Meloidogyne hapla KC287195.1.520 Meloidogyne hapla AY757853.1.636 Meloidogyne hapla AY757856.1.636 Meloidogyne hapla AY919173.1.636 Meloidogyne hapla AY919169.1.636 Meloidogyne hapla AY757859.1.636 Meloidogyne hapla AY757855.1.636 Meloidogyne hapla AY919177.1.636 Meloidogyne hapla AY757861.1.636 Meloidogyne hapla KC287194.1.520 Meloidogyne hapla AY757854.1.636 Meloidogyne hapla AY919172.1.636 Meloidogyne hapla AY919171.1.636 Meloidogyne hapla AY757849.1.636 Meloidogyne hapla AY757852.1.636 Meloidogyne hapla AY757850.1.636 Meloidogyne hapla AY757857.1.636 Meloidogyne hapla AY757851.1.636 Meloidogyne hapla AY757862.1.636 Meloidogyne hapla AY757865.1.636 Meloidogyne hapla AY757860.1.636 Meloidogyne hapla AY757864.1.636 Meloidogyne hapla AY919170.1.636 Meloidogyne hapla AY757866.1.636 Meloidogyne hapla AF442194.1.1580 Meloidogyne hapla EU669941.1.1685 Meloidogyne hapla ABLG01003413.1200.2052 Meloidogyne hapla EU669943.1.1687 Meloidogyne hapla AY593898.1.1689 Meloidogyne hapla AY593893.1.1689 Meloidogyne partityla AY919183.1.635 Meloidogyne partityla AY757874.1.635 Meloidogyne dunensis EF612713.1.830 Meloidogyne spartinae EF189177.1.1664 Meloidogyne cf. graminis TSH-2004 AY757848.1.636 Meloidogyne marylandi JN241856.1.1501 Meloidogyne marylandi JN241848.1.605 Meloidogyne marylandi JN241833.1.605 Meloidogyne marylandi JN241850.1.605 Meloidogyne marylandi JN241844.1.602 Meloidogyne marylandi JN241852.1.606 Meloidogyne cf. graminis TSH-2005 AY919168.1.636 Meloidogyne cf. graminis TSH-2005 AY919167.1.636 Meloidogyne cf. graminis TSH-2004 AY757847.1.636 Meloidogyne graminis AY919166.1.637 Meloidogyne graminis AY757846.1.637 Meloidogyne graminis AY757845.1.637 Meloidogyne graminis AY919165.1.637 Meloidogyne graminis JN241837.1.609 Meloidogyne graminis JN241835.1.603 Meloidogyne graminis JN241834.1.606 Meloidogyne graminis JN241854.1.605 Meloidogyne graminis JN241843.1.606 Meloidogyne graminis JN241851.1.606 Meloidogyne graminis JN389786.1.1530 Meloidogyne graminis JN241838.1.1531 Meloidogyne maritima EU669945.1.1689 Meloidogyne maritima AF442199.1.1581 Meloidogyne maritima EU669944.1.1690 Meloidogyne microtyla AF442198.1.1577 Meloidogyne ardenensis AY593894.1.1688 Meloidogyne ardenensis EU669946.1.1688 Meloidogyne silvestris EU570215.1.772 Meloidogyne hapla ABLG01002648.6192.7987 Meloidogyne duytsi AF442197.1.1580 Meloidogyne hapla ABLG01003285.9.1790 Meloidogyne hapla ABLG01000304.4568.6351 Meloidogyne incognita (southern root-knot nematode) CABB01001004.7271.9048 Meloidogyne incognita (southern root-knot nematode) AF535868.1.1577 Meloidogyne incognita (southern root-knot nematode) U81578.1.1706 Meloidogyne incognita (southern root-knot nematode) CABB01000745.17894.19671 Meloidogyne incognita (southern root-knot nematode) CABB01000685.3215.4987 Meloidogyne incognita (southern root-knot nematode) CABB01000266.15199.16972 Meloidogyne incognita (southern root-knot nematode) CABB01000070.25707.27482 Meloidogyne incognita (southern root-knot nematode) CABB01000382.11785.13533 Meloidogyne sp. Pak.P.R.37 JQ806350.1.381 Meloidogyne incognita (southern root-knot nematode) CABB01001290.10393.12124 Meloidogyne incognita (southern root-knot nematode) CABB01000700.18614.20385 Meloidogyne incognita (southern root-knot nematode) CABB01000687.5455.7230 Meloidogyne incognita (southern root-knot nematode) KC875376.1.1679 Meloidogyne incognita (southern root-knot nematode) CABB01006461.3014.3968 Meloidogyne mayaguensis AY757873.1.637 Meloidogyne mayaguensis AY919182.1.637 Meloidogyne mayaguensis AY446966.1.637 Meloidogyne mayaguensis AY446965.1.637 Meloidogyne mayaguensis AY446967.1.637 Meloidogyne mayaguensis AY446968.1.637 Meloidogyne incognita (southern root-knot nematode) CABB01000014.68164.69417 Meloidogyne incognita (southern root-knot nematode) CABB01003807.5436.6680 Meloidogyne incognita (southern root-knot nematode) CABB01006032.1321.2681 Meloidogyne incognita (southern root-knot nematode) CABB01000105.28083.29440 Meloidogyne incognita (southern root-knot nematode) CABB01000105.39471.40831 Meloidogyne artiellia AF248477.457.2253 Meloidogyne artiellia KC875392.1.1711 Meloidogyne artiellia KC875391.1.1710 Meloidogyne artiellia AF442192.1.1597 Meloidogyne mali EU669949.1.1702 Meloidogyne mali KC875395.1.1704 Meloidogyne mali JX978225.1.1744 Meloidogyne mali EU669947.1.1703 Meloidogyne mali KF895399.1.767 Meloidogyne mali KF895398.1.767 Meloidogyne mali KF895400.1.767 Meloidogyne mali EU669948.1.1705 Meloidogyne mali KF895397.1.767 Meloidogyne sp. MHMH-2008 EU669952.1.1729 Meloidogyne sp. MHMH-2008 EU669950.1.1729 Meloidogyne sp. MHMH-2008 EU669951.1.1729 Meloidogyne coffeicola HE667739.1.1985 Meloidogyne camelliae JX912884.1.915 Meloidogyne ichinohei KC875386.1.1576 Meloidogyne ichinohei KC875385.1.1576 Meloidogyne ichinohei AF442191.1.1582 Meloidogyne ichinohei EU669954.1.1692 Meloidogyne ichinohei EU669953.1.1692 Meloidogyne incognita (southern root-knot nematode) CABB01000824.10584.12358 Meloidogyne incognita (southern root-knot nematode) CABB01000776.18892.20669 Meloidogyne incognita (southern root-knot nematode) CABB01001346.7708.9483 Meloidogyne incognita (southern root-knot nematode) JX100421.1.1664 Meloidogyne ethiopica JF330237.1.541 Meloidogyne haplanaria AY919178.1.637 Meloidogyne haplanaria AY757867.1.637 Meloidogyne ethiopica KC551945.1.1602 Meloidogyne ethiopica FJ559408.1.1626 Meloidogyne ethiopica JF330247.1.701 Meloidogyne ethiopica JF330242.1.613 Meloidogyne hispanica HE667741.1.1931 Meloidogyne incognita (southern root-knot nematode) CABB01005760.2553.4328 Meloidogyne incognita (southern root-knot nematode) CABB01000393.21272.23049 Meloidogyne ethiopica JQ768373.1.1673 Meloidogyne incognita (southern root-knot nematode) CABB01000393.6536.8311 Meloidogyne incognita (southern root-knot nematode) CABB01000393.13387.15162 Meloidogyne hispanica EU443609.1.779 Meloidogyne hispanica EU443610.1.782 Meloidogyne hispanica EU443611.1.1223 Meloidogyne incognita (southern root-knot nematode) CABB01006749.1.1669 Meloidogyne sp. 38 AY942633.1.1662 Meloidogyne ethiopica AY942630.1.1649 Meloidogyne javanica (root-knot nematode) JX100422.1.1664 Meloidogyne ethiopica JF330248.1.701 Meloidogyne incognita (southern root-knot nematode) JF330245.1.701 Meloidogyne arabicida AY942625.1.1633 Meloidogyne arabicida HE667738.1.1893 Meloidogyne konaensis HE667744.1.1898 Meloidogyne paranaensis AY942622.1.1642 Meloidogyne izalcoensis HE667743.1.1831 Meloidogyne sp. MS3 AY942636.1.1638 Meloidogyne javanica (root-knot nematode) JQ026519.1.850 Meloidogyne sp. AC-2011 JF330241.1.611 Meloidogyne incognita (southern root-knot nematode) JF330238.1.542 Meloidogyne incognita (southern root-knot nematode) JF330243.1.701 Meloidogyne sp. AC-2011 JF330246.1.701 Meloidogyne incognita (southern root-knot nematode) JF330244.1.701 Meloidogyne arenaria DQ080578.1.637 Meloidogyne javanica (root-knot nematode) AY757872.1.637 Meloidogyne cf. arenaria TSH-2004 AY757834.1.637 Meloidogyne cf. incognita TSH-2004 AY757870.1.637 Meloidogyne cf. arenaria TSH-2004 AY757833.1.637 Meloidogyne incognita (southern root-knot nematode) HQ709102.1.868 Meloidogyne hapla AY593891.1.554 Meloidogyne javanica (root-knot nematode) AY919180.1.637 Meloidogyne javanica (root-knot nematode) AY757871.1.637 Meloidogyne cf. incognita TSH-2004 AY757868.1.637 Meloidogyne cf. arenaria TSH-2004 AY757832.1.637 Meloidogyne cf. incognita TSH-2005 AY919179.1.637 Meloidogyne javanica (root-knot nematode) AF442193.1.1578 Meloidogyne javanica (root-knot nematode) AY919181.1.637 Meloidogyne morocciensis AY942632.1.1650 Meloidogyne sp. Pak.P.R.m2 JQ806346.1.874 Meloidogyne sp. Pak.S.R.25 JQ806349.1.874 Meloidogyne incognita (southern root-knot nematode) JQ806342.1.876 Meloidogyne incognita (southern root-knot nematode) JQ806341.1.876 Meloidogyne incognita (southern root-knot nematode) JQ806344.1.875 Meloidogyne javanica (root-knot nematode) JQ806345.1.875 Meloidogyne incognita (southern root-knot nematode) JQ731888.1.876 Meloidogyne incognita (southern root-knot nematode) JQ731889.1.868 Meloidogyne incognita (southern root-knot nematode) JQ806340.1.877 Meloidogyne javanica (root-knot nematode) EU669938.1.1685 Meloidogyne sp. 50 AY942635.1.1656 Meloidogyne arenaria KF112872.1.637 Meloidogyne incognita (southern root-knot nematode) AY942624.1.1656 Meloidogyne floridensis AY942621.1.1655 Meloidogyne arenaria AY942623.1.1614 Meloidogyne javanica (root-knot nematode) AY942626.1.1646 Meloidogyne incognita (southern root-knot nematode) JX100420.1.1665 Meloidogyne sp. 40 AY942634.1.1659 Meloidogyne incognita (southern root-knot nematode) EU669939.1.1686 Meloidogyne incognita (southern root-knot nematode) AY268120.1.1754 Meloidogyne arenaria AY268118.1.1755 Meloidogyne javanica (root-knot nematode) AY268121.1.1756 Meloidogyne sp. AC-2011 JF330239.1.542 Meloidogyne arenaria U42342.740.2527 Meloidogyne arenaria AF535867.1.1578 Meloidogyne hapla AY593890.1.966 Meloidogyne incognita (southern root-knot nematode) EU669940.1.1654 Meloidogyne incognita (southern root-knot nematode) CABB01002720.5723.7498 Meloidogyne incognita (southern root-knot nematode) AY284621.1.1704 Meloidogyne cf. incognita TSH-2004 AY757869.1.637 Meloidogyne sp. AC-2011 JF330252.1.701 Meloidogyne sp. AC-2011 JF330251.1.701 Meloidogyne sp. AC-2011 JF330250.1.695 Meloidogyne sp. AC-2011 JF330240.1.515 Meloidogyne incognita (southern root-knot nematode) JF330249.1.519 Meloidogyne javanica (root-knot nematode) JX100419.1.1666 Meloidogyne incognita (southern root-knot nematode) JQ806343.1.874 Meloidogyne sp. Brito DPI I DQ080580.1.637 Meloidogyne mayaguensis AY942629.1.1656 Meloidogyne exigua AY942627.1.1620 Meloidogyne exigua AF442200.1.1581 Meloidogyne exigua HQ709101.1.868 Meloidogyne oryzae AY942631.1.1653 Meloidogyne graminicola KF201168.1.1586 Meloidogyne cf. graminicola TSH-2005 AY919161.1.639 Meloidogyne cf. graminicola TSH-2005 AY919160.1.639 Meloidogyne cf. graminicola TSH-2005 AY919163.1.639 Meloidogyne cf. graminicola TSH-2005 AY919164.1.639 Meloidogyne cf. graminicola TSH-2005 AY919162.1.639 Meloidogyne cf. graminicola TSH-2004 AY757844.1.639 Meloidogyne graminicola AF442196.1.1579 Meloidogyne naasi AY593900.1.1693 Meloidogyne naasi JN241841.1.1566 Meloidogyne naasi AY593901.1.1693 Meloidogyne naasi AY593902.1.1694 Meloidogyne naasi JN241846.1.612 Meloidogyne naasi JN241847.1.611 Meloidogyne naasi JN241855.1.611 Meloidogyne naasi JN241853.1.608 Meloidogyne naasi JN241842.1.608 Meloidogyne naasi JN389790.1.604 Meloidogyne naasi JN241845.1.607 Meloidogyne naasi JN241836.1.607 Meloidogyne naasi JN241849.1.605 Meloidogyne minor EU669937.1.1692 Meloidogyne minor JN389787.1.1543 Meloidogyne minor JN241840.1.1497 Meloidogyne minor JN389791.1.599 Meloidogyne minor JN241839.1.1692 Meloidogyne minor AY593899.1.1693 Meloidogyne minor JN389792.1.600 Meloidogyne minor JN241832.1.629 Meloidogyne chitwoodi AY593884.1.1691 Meloidogyne fallax EU669936.1.1691 Meloidogyne fallax AY593895.1.1691 Meloidogyne fallax EU669935.1.1689 Meloidogyne chitwoodi AY593885.1.1692 Meloidogyne chitwoodi AY593889.1.1693 Meloidogyne chitwoodi AY593887.1.1692 Meloidogyne fallax JN389788.1.1521 Meloidogyne fallax JN389789.1.527 Meloidogyne chitwoodi EU669933.1.1692 Meloidogyne chitwoodi AY593886.1.1692 Meloidogyne chitwoodi EU669932.1.1692 Meloidogyne chitwoodi AY593888.1.1695 Meloidogyne fallax AY593896.1.644 Meloidogyne chitwoodi EU669934.1.1693 Meloidogyne chitwoodi AY146458.1.636 Meloidogyne cf. fallax TSH-2004 AY757843.1.636 Meloidogyne chitwoodi AY757838.1.636 Meloidogyne chitwoodi AY757835.1.636 Meloidogyne chitwoodi AY757840.1.636 Meloidogyne cf. chitwoodi TSH-2004 AY757842.1.635 Meloidogyne cf. chitwoodi TSH-2005 AY919159.1.635 Meloidogyne chitwoodi AY593883.1.1693 Meloidogyne chitwoodi AY919154.1.636 Meloidogyne chitwoodi AY919157.1.636 Meloidogyne chitwoodi AY757839.1.636 Meloidogyne chitwoodi DQ080579.1.636 Meloidogyne chitwoodi AY757841.1.636 Meloidogyne chitwoodi AY919155.1.636 Meloidogyne chitwoodi AY919158.1.636 Meloidogyne chitwoodi AY919156.1.636 Meloidogyne chitwoodi AY757836.1.636 Meloidogyne chitwoodi AY757837.1.636 Meloidogyne chitwoodi AY919153.1.636 Meloidogyne chitwoodi JN632480.1.605 Meloidogyne chitwoodi AF442195.1.1578 0.11 0.11

Repeat the whole analysis while excluding some sequence

The list of IDs is now passed to the exclude keyword and they will not be read into the Project:

In [31]:
# Start a project with an 18S locus
pj = Project([Locus('dna','rRNA','18s',['18s'])])

# Read the SILVA alignemnt while excluding three sequences
pj.read_alignment('data/arb-silva.de_2014-11-17_id215613_gapcompressedvertical.fasta',
                  'dna','rRNA','18s',
                  exclude=['ABLG01003097.925.2722',
                           'CABB01001290.10393.12124',
                           'JQ806350.1.381'])

# Edit the qualifiers as above to create an organism qualifier
pj.add_qualifier_from_source('original_desc')
for record in pj.records:
    for feature in record.features:
        feature.qualifiers['organism'] = [feature.qualifiers['original_desc'][0].split(';')[-1]]

# Trim the alignment        
manual = TrimalConf(pj, method_name='manual' ,trimal_commands={'gapthreshold': '0.5'})
pj.trim([manual])

# Build the tree
raxml = RaxmlConf(pj, method_name='fD_fb', preset='fD_fb', threads=6)
pj.tree([raxml])

#Annotate the tree as before
pj.annotate('.', 'mid', 'mid', ['organism'], node_support_dict=supports, scale=2000)

# Checkpoint the analysis
pickle_pj(pj, 'meloidogyne.ckp')

# Archive the analysis
publish(pj, 'meloidogyne', '.')
trimal -in 454721416256290.0_18s@ReadDirectly.fasta -gapthreshold 0.5
raxmlHPC-PTHREADS-SSE3 -f D -m GTRGAMMA -n 340991416256292.48_18s@ReadDirectly@manual0 -p 846 -s 340991416256292.48_18s@ReadDirectly@manual.fasta -T 6 -N 1
raxmlHPC-PTHREADS-SSE3 -f b -m GTRGAMMA -n 340991416256292.48_18s@ReadDirectly@manual1 -p 386 -s 340991416256292.48_18s@ReadDirectly@manual.fasta -t RAxML_bestTree.340991416256292.48_18s@ReadDirectly@manual0 -T 6 -z RAxML_rellBootstrap.340991416256292.48_18s@ReadDirectly@manual0
<html>
rooting tree 18s@ReadDirectly@manual@fD_fb at midpoint
<A href=./340991416256292.48_18s@ReadDirectly@manual.png>340991416256292.48_18s@ReadDirectly@manual</A><BR>
DEBUG:Cloud:Log file (/home/amir/.picloud/cloud.log) opened
DEBUG:Cloud:Deleting 12553.log (7.87048627344 days old)
DEBUG:Cloud:Deleting 12553.lock (7.87048627344 days old)


</html>
.
checking if file exists
reporter was called by publish
now printing species table
now making sequence statistics plots
now reporting concatenations
now reporting methods
now reporting alignment statistics
making RF matrix
reporting trees
pickling
archiving
report ready

/usr/local/lib/python2.7/dist-packages/pandas/io/excel.py:626: UserWarning: Installed openpyxl is not supported at this time. Use >=1.6.1 and <2.0.0.
  .format(openpyxl_compat.start_ver, openpyxl_compat.stop_ver))

Here is the resulting tree without the excluded sequences. We are looking at the png file and not rendering the object because the object does not retain the tree style which also includes the scaling. Therefore, in the figure, the tree is wider. It seems that there are some incognita's that have long branches and the alignment should be closely inspected.

In [34]:
from IPython.display import Image
Image('340991416256292.48_18s@ReadDirectly@manual.png')
Out[34]:
In []: